Search based on experiment type. database field. More specific search options. Use wildcard (*) before and after text

Transcription

1 Querying and Performing Comparisons Shannon Dalton April 2011

2 Overview Query Local/National Databases Simple query Query Tools Use for National database Perform Comparisons Add/remove/rearrange entries Dendrograms Save/load comparisons

3 Simple Query Search based on experiment type Search based on database field More specific search options Use wildcard (*) before and after text

4 Simple Query Click on the Binoculars Icon in Main Window Search yields all isolates in your local database that have 2009 as the Upload Date

5 Query by PulseNet Tools To start, click on the PulseNet tools icon. Note: This option is useful to see all available query options and modify field options. Be very careful using this script.

6 Query by Isolate To start, click on the Query by Isolate icon. Note: This option is useful for demographicsbased searches. Allows for the use of drop-down menus. Enter Search Criteria. (Ex: Date Range) Click Replace List

7 Hot List Tool A Hot List search can be used to show all recently uploaded isolates within your local database NOTE: the isolates must have an upload date for this query to work Click on Hot List icon and enter number of days (Ex. 60 days). Why? You want to see what has been uploaded in the past 60 days

8 Hot List Tool Isolates submitted within the past 60 days will be selected

9 Query Tools for National Databases Isolate Query: Hot List : National List: Temporarily Download Selected Entries to local database Pattern Query: Delete Selected Entries: Show Recent Matches: NOTE: Queries within the national database will only look within the number of days you re connected to

10 Narrow Your Search The results of your hot-list search will appear. Important! It may be a LARGE number of entries! You do not need to view or download all of them. Downloading an entire 60-day search wastes time and server space, and may cause your database to time out. Therefore, think about what you REALLY need and narrow your search! Ex: 60 Day Hot List Search Wow! 1515 isolates! I need to narrow my search before I download anything

11 Narrow Your Search Use query tools or the Select entries at server database icon to narrow your search Ex: Search to include only isolates of the particular serotype that you are looking for Search in List (your list includes the 1515 that were selected from your original hot-list search)

12 Narrow Your Search After narrowing your search, you have a smaller number of isolates that will not take as long to download

13 Download Entries Click on Download selected entries from server icon to download to your local database Isolate(s) will be downloaded temporarily in the form of a bundle

14 Create New Comparison Select isolates for comparison, then go to Create new comparison under the Comparison menu

15 Create New Comparison Notice number of entries

16 View Experiment Patterns Choose enzyme from pull-down menu Click on the Show Image icon in top toolbar, or choose enzyme from the Experiments panel to show pattern images

17 Arrange Entries by Field Right-click on field (ex. Serotype) and choose Arrange entries by field

18 Arrange Entries by Field Notice that the entries are arranged by serotype in alphabetical order

19 Bring Selected Entries to Top Another view of selected entries within a comparison: go to Edit and select Bring selected entries to top

20 Bring Selected Entries to Top Now the selected entries are at the top of the comparison

21 Freeze Left Pane To set a column to be fixed, right click on the column before the column to be fixed By freezing a column, all columns located before highlighted column will also be stationary

22 Freeze Left Pane Notice the line in front of the highlighted column You can use the cursor to scroll through the other database fields

23 Copy and Paste in a Comparison If you want to add patterns to a comparison window: Click Copy selection in main window or another comparison window Click Paste selection in comparison window

24 Cut in a Comparison If you want to take patterns out of a comparison window: Select the patterns Click Cut selection in comparison window Click OK

25 Show Band Markings Click on Show bands icon in top toolbar to show band markings

26 Click on Show metric scale icon in top toolbar to show band markings Show Metric Scale

27 Perform Cluster Analysis Click on Calculate cluster analysis

28 Cluster Analysis Parameters PulseNet Parameters for Cluster Analysis

29 Dendrogram

30 Cluster Analysis Parameters: Position Tolerance Computer Interpretation of Band Positions To the computer a band is not a band, but a band plus a window surrounding the band When comparing band positions of two profiles the computer will consider the band position identical if the band position in one of the profiles falls within a window around a band in the other profile = = The size of this window is called the Position Tolerance (set at 1.5% of the run length of the band)

31 Cluster Analysis Parameters: Position Tolerance Set Too High The computer will interpret some unique profiles as being identical!

32 Save a Comparison Click Save to save your comparison Name your comparison and Click OK

33 Compare One Pattern to Others Click to highlight one isolate (key) within your comparison to compare it to others in your comparison

34 Compare One Pattern to Others Click on Arrange by decreasing similarity to compare the highlighted pattern to all others within the comparison window

35 Compare One Pattern to Others If this screen appears, click Yes

36 Compare One Pattern to Others % Similarity Now, your patterns are arranged by decreasing similarity to the pattern you selected

37 REMINDER: The Computer is Just a Tool Your Eyes Always Determine Whether Patterns are Indistinguishable or Different

38 Questions? Thank you for your attention The findings and conclusions in this presentation are those of the author and do not necessarily represent the views of the Centers for Disease Control and Prevention

39 Exercise 4